Next generation sequencing analysis of double-stranded RNAs from sweet cherry powdery mildew fungus Podosphaera prunicola

Pandey, Binod; Naidu, Rayapati A.; Grove, Gary G.

doi:10.1007/s42161-018-0092-0

Cited by 11 publications

(9 citation statements)

References 46 publications

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“…A virus sequence was identified in an Acidomyces richmondensis sample (PRJNA250470; unpublished) with a single segment genome sequence, 10,291 nt in length, that encoded four predicted ORFs (Table 1). The gene product from ORF2 contains the RdRP domain (Fig 7B) and a BLAST-P search of the ‘nr’ database with this sequence identified two related, full length mycoviruses, Macrophomina phaseolina tobamo-like virus 1 (MpTlV1) [5] and Podosphaera prunicola tobamo-like virus 1 (PpTlV1) [66]. As such, this newly identified virus has been named Acidomyces richmondensis tobamo-like virus 1 (ArTlV1).…”

Section: Resultsmentioning

confidence: 99%

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

et al. 2019

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The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.

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Section: Resultsmentioning

confidence: 99%

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

et al. 2019

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“…prunicola for a powdery mildew from Prunus melanocarpa , that also parasitizes Prunus virginiana , Prunus serotina , and P . avium (Pandey et al, 2018). Based on morphological and phylogenetic analysis, Moparthi et al (2019) recently described P. cerasi on P. avium as a separate species, distinguished from P .…”

Section: Introductionmentioning

confidence: 99%

“…avium (Pandey et al, 2018). Based on morphological and phylogenetic analysis, Moparthi et al (2019) recently described P. cerasi on P. avium as a separate species, distinguished from P. clandestina in the strict sense on Crataegus and P. prunicola.…”

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confidence: 99%

Molecular data from up to 130‐year‐old herbarium specimens do not support the presence of cherry powdery mildew in Australia

et al. 2020

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Powdery mildews are some of the most commonly occurring obligate plant pathogens worldwide, with approximately 900 species and 19 genera infecting over 10,000 plant species including ornamental, agricultural, and horticultural plants (Braun & Cook, 2012; Kiss et al., 2020; Marmolejo et al., 2018). Horticulture in Australia was established by the immigration of European and Asian settlers who introduced horticultural plant species from Europe, Asia, and the Americas (Kiss et al., 2020; Virtue et al., 2004). The introduction of exotic plant species to a new environment also brought exotic plant pathogens, including powdery mildews (Brewer & Milgroom, 2010;

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“…Advanced mycovirus studies are now focused on providing data on the host transcriptome and RNA signaling [31,68,80]. HTS has been successfully used to detect known and unknown viruses from fungal samples [81] as well as detect mycovirus genome segments through small RNA deep sequencing [25,82]. In addition, host transcriptome and small RNA profiling data have provided insight into the molecular mechanisms underpinning the observed changes in phenotype [83,84].…”

Section: Metagenomic Studies Of Fungal Endophytes and Their Mycovirusesmentioning

confidence: 99%

Viruses of endophytic and pathogenic forest fungi

Siddique

2020

Virus Genes

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Mycoviruses, just as the fungal endophytes they infect, are ubiquitous biological entities on Earth. Mycoviruses constitute a diverse group of viruses, and metagenomic approaches have-through recent discoveries of been mycoviruses-only recently began to provide evidence of this astonishing diversity. The current review presents (1) various mycoviruses which infect fungal endophytes and forest pathogens, (2) their presumed origins and interactions with fungi, plants and the environment, (3) high-throughput sequencing techniques that can be used to explore the horizontal gene transfer of mycoviruses, and (4) how the hypo-and hypervirulence induced by mycoviral infection is relevant to the biological control of pathogenic fungi.

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Next generation sequencing analysis of double-stranded RNAs from sweet cherry powdery mildew fungus Podosphaera prunicola

Cited by 11 publications

References 46 publications

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

Molecular data from up to 130‐year‐old herbarium specimens do not support the presence of cherry powdery mildew in Australia

Viruses of endophytic and pathogenic forest fungi

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